lpqB Resolved · high auto-curated
H37Rv Rv3244c · MTBC0 mtbc0_003452 ·
583 aa · 3645302–3647053 (-) ·
RefSeq NP_217761.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqB |
|---|---|
| MTBC0 PGAP re-annotation | MtrAB system accessory lipoprotein LpqB |
| Revised (this work) | MtrAB system accessory lipoprotein LpqB. Pfam: LpqB_N (PF25976.1), Germane (PF10646.15), Gmad1 (PF10647.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK37
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lipoprotein LpqB |
| Curated function | May modulate activity of the MtrAB system in controlling homeostasis of the cell wall and cell division (By similarity). Partially restores antibiotic resistance to M.smegmatis in which this gene has been disrupted. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqB |
| eggNOG description | Lipoprotein lpqB |
| Orthologous group | COG5401 |
| Gene Ontology (11) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.156 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 3 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
LpqB_N | PF25976.1 | 4.0e-25 | 41–161 | Lipoprotein LpqB, N-terminal domain |
Germane | PF10646.15 | 2.8e-16 | 168–290 | Sporulation and spore germination |
Gmad1 | PF10647.16 | 3.1e-77 | 323–582 | Lipoprotein LpqB beta-propeller domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mtrB (two component sensory histidine kinase MtrB), high confidence from genomic context alone (score 949 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3245c mtrB |
two component sensory histidine kinase MtrB | 979 | 949 ctx | neighborhood:816 coexpression:651 textmining:621 |
Rv3246c mtrA |
two component DNA-binding response regulator MtrA | 936 | 820 ctx | neighborhood:814 textmining:661 |
Rv3243c hyp |
hypothetical protein | 803 | 803 ctx | neighborhood:796 |
Rv3802c |
membrane protein | 774 | 774 ctx | cooccurence:764 |
Rv1275 lprC |
lipoprotein LprC | 768 | 768 ctx | cooccurence:765 |
Rv3668c |
protease | 768 | 768 ctx | cooccurence:762 |
Rv0383c ttfA hyp |
hypothetical protein | 764 | 764 ctx | cooccurence:764 |
Rv3794 embA |
arabinosyltransferase A | 759 | 760 ctx | cooccurence:756 |
Rv1476 |
membrane protein | 757 | 758 ctx | cooccurence:756 |
Rv3035 hyp |
hypothetical protein | 757 | 757 ctx | cooccurence:752 |
Rv1274 lprB |
lipoprotein LprB | 756 | 757 ctx | cooccurence:755 |
Rv3795 embB |
arabinosyltransferase B | 753 | 754 ctx | cooccurence:750 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 753 | 754 ctx | cooccurence:753 |
Rv3247c tmk |
thymidylate kinase | 748 | 749 ctx | neighborhood:748 |
Rv3793 embC |
arabinosyltransferase C | 744 | 744 ctx | cooccurence:741 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: lipoprotein LpqB
- MTBC0 PGAP product: MtrAB system accessory lipoprotein LpqB
- Pfam (hmmscan --cut_ga): LpqB_N PF25976.1 (E=4e-25), Germane PF10646.15 (E=3e-16), Gmad1 PF10647.16 (E=3e-77)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217761.1)
- Domains: Pfam-A via hmmscan --cut_ga — LpqB_N (PF25976.1), Germane (PF10646.15), Gmad1 (PF10647.16)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG5401 - Curated reference: UniProt P9WK37 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
161 functional partner(s); context anchor
mtrB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003452|Rv3244c|lpqB MRLTILLFLGAVLAGCASVPSTSAPQAIGTVERPVPSNLPKPSPGMDPDVLLREFLKATADPANRHLAARQFLTESASNAWDDAGSALLIDHVVFVETRSAEKVSVTMRADILGSLSDVGVFETAEGQLPDPGPIELVKTSGGWRIDRLPNGVFLDWQQFQETYKRNTLYFADPTGKTVVPDPRYVAVSDRDQLATELVSKLLAGPRPEMARTVRNLLAPPLRLRGPVTRADGGKSGIGRGYGGARVDMEKLSTTDPHSRQLLAAQIIWTLARADIRGPYVINADGAPLEDRFAEGWTTSDVAATDPGVADGAAAGLHALVNGSLVAMDAQRVTPVPGAFGRMPEQTAAAVSRSGRQVASVVTLGRGAPDEAASLWVGDLGGEAVQSADGHSLSRPSWSLDDAVWVVVDTNVVLRAIQDPASGQPARIPVDSTAVASRFPGAINDLQLSRDGTRAAMVIGGQVILAGVEQTQAGQFALTYPRRLGFGLGSSVVSLSWRTGDDIVVTRTDAAHPVSYVNLDGVNSDAPSRGLQTPLTAIAANPSTVYVAGPQGVLMYSASVESRPGWADVPGLMVPGAAPVLPG